Mapping the resistance-associated mobilome of a carbapenem-resistant Klebsiella pneumoniae strain reveals insights into factors shaping these regions and facilitates generation of a 'resistance-disarmed' model organism

Objectives
This study aims to investigate the landscape of mobile genome, with a focus on antibiotic resistance-associated factors in carbapenem-resistant Klebsiella pneumoniae. Methods
The mobile genome of the completely sequenced K. pneumoniae HS11286 strain, a ST11 carbapenem-resistant, near pan-resistant clinical isolate, was annotated in fine detail. The identified mobile genetic elements were mapped to the genetic contexts of resistance genes. The blaKPC-2 gene and a 26-kb region containing 12 clustered antibiotic resistance genes and one biocide resistance gene were deleted, and the MICs were tested again to ensure antibiotic resistance was lost.Results
HS11286 contains six plasmids, 49 insertion sequences (ISs), nine transposons, two separate In2-related integron remnants, two integrative and conjugative elements (ICEs), and seven prophages. Sixteen plasmid-borne resistance genes were identified, of which fourteen were found directly associated with Tn1721, Tn3, Tn5393, In2, ISCR2 and ISCR3-derived elements. IS26 appears to have actively moulded several of these genetic regions. Deletion of blaKPC-2, followed by that of a 26-kb region containing 12 clustered antibiotic resistance genes, progressively decreased the spectrum and level of resistance exhibited by the resultant mutant strains.Conclusion
This study has reiterated the role of plasmids as bearers of the vast majority of resistance genes in this species, and provided valuable insights as to the vital role played by ISs, transposons and integrons in shaping the resistance-coding regions in this important strain. The 'resistance-disarmed' K. pneumoniae ST11 strain generated in this study will offer a more benign and readily genetically-modifiable model organism for future extensive functional studies.